1
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Goldner Kabeli R, Zevin S, Abargel A, Zilberberg A, Efroni S. Self-supervised learning of T cell receptor sequences exposes core properties for T cell membership. SCIENCE ADVANCES 2024; 10:eadk4670. [PMID: 38669334 DOI: 10.1126/sciadv.adk4670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The T cell receptor (TCR) repertoire is an extraordinarily diverse collection of TCRs essential for maintaining the body's homeostasis and response to threats. In this study, we compiled an extensive dataset of more than 4200 bulk TCR repertoire samples, encompassing 221,176,713 sequences, alongside 6,159,652 single-cell TCR sequences from over 400 samples. From this dataset, we then selected a representative subset of 5 million bulk sequences and 4.2 million single-cell sequences to train two specialized Transformer-based language models for bulk (CVC) and single-cell (scCVC) TCR repertoires, respectively. We show that these models successfully capture TCR core qualities, such as sharing, gene composition, and single-cell properties. These qualities are emergent in the encoded TCR latent space and enable classification into TCR-based qualities such as public sequences. These models demonstrate the potential of Transformer-based language models in TCR downstream applications.
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Affiliation(s)
- Romi Goldner Kabeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Zevin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Abargel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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2
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Luo Y, Li T, Zhao H, Chen A. A novel 7‑hypoxia‑related long non‑coding RNA signature associated with prognosis and proliferation in melanoma. Mol Med Rep 2022; 26:255. [PMID: 35703357 PMCID: PMC9218734 DOI: 10.3892/mmr.2022.12771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/12/2022] [Indexed: 11/05/2022] Open
Abstract
Hypoxia‑related long non‑coding RNAs (lncRNAs) are important indicators of the poor prognosis of cancers. The present study aimed to explore the potential relationship between melanoma and hypoxia‑related lncRNAs. The transcriptome and clinical data of patients with melanoma were downloaded from The Cancer Genome Atlas database. The prognostic hypoxia‑related lncRNAs were screened out using Pearson's correlation test and univariate Cox analysis. As a result, a hypoxia‑related‑lncRNA signature based on the expression of 7 lncRNAs was constructed, with one unfavourable [MIR205 host gene (MIR205HG)] and six favourable (T cell receptor β variable 11‑2, HLA‑DQB1 antisense RNA 1, AL365361.1, AC004847.1, ubiquitin specific peptidase 30 antisense RNA 1 and AC022706.1) lncRNAs as prognostic factors for melanoma. Patients with melanoma were divided into high‑ and low‑risk groups based on the risk score obtained. Survival analyses were performed to assess the prognostic value of the present risk model. Potential tumour‑associated biological pathways associated with the present signature were explored using gene set enrichment analysis. The CIBERSORT algorithm demonstrated the important role of the hypoxia‑related lncRNAs in regulating tumour‑infiltrating immune cells. Clinical samples collected from our center partly confirmed our findings. Cell Counting Kit‑8 and flow cytometry assays indicated the suppression of proliferation of melanoma cells following inhibition of MIR205HG expression. Indicators of the canonical Wnt/β‑catenin signalling pathway were detected by western blotting. The present study demonstrated that MIR205HG could promote melanoma cell proliferation partly via the canonical Wnt/β‑catenin signalling pathway. These findings indicated a 7‑hypoxia‑related‑lncRNA signature that can serve as a novel predictor of melanoma prognosis.
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Affiliation(s)
- Yi Luo
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tinghao Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Hengguang Zhao
- Department of Dermatology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
| | - Aijun Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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3
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Katayama Y, Kobayashi TJ. Comparative Study of Repertoire Classification Methods Reveals Data Efficiency of k -mer Feature Extraction. Front Immunol 2022; 13:797640. [PMID: 35936014 PMCID: PMC9346074 DOI: 10.3389/fimmu.2022.797640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/20/2022] [Indexed: 01/18/2023] Open
Abstract
The repertoire of T cell receptors encodes various types of immunological information. Machine learning is indispensable for decoding such information from repertoire datasets measured by next-generation sequencing (NGS). In particular, the classification of repertoires is the most basic task, which is relevant for a variety of scientific and clinical problems. Supported by the recent appearance of large datasets, efficient but data-expensive methods have been proposed. However, it is unclear whether they can work efficiently when the available sample size is severely restricted as in practical situations. In this study, we demonstrate that their performances can be impaired substantially below critical sample sizes. To complement this drawback, we propose MotifBoost, which exploits the information of short k-mer motifs of TCRs. MotifBoost can perform the classification as efficiently as a deep learning method on large datasets while providing more stable and reliable results on small datasets. We tested MotifBoost on the four small datasets which consist of various conditions such as Cytomegalovirus (CMV), HIV, α-chain, β-chain and it consistently preserved the stability. We also clarify that the robustness of MotifBoost can be attributed to the efficiency of k-mer motifs as representation features of repertoires. Finally, by comparing the predictions of these methods, we show that the whole sequence identity and sequence motifs encode partially different information and that a combination of such complementary information is necessary for further development of repertoire analysis.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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4
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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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5
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Agathangelidis A, Vlachonikola E, Davi F, Langerak AW, Chatzidimitriou A. High-Throughput immunogenetics for precision medicine in cancer. Semin Cancer Biol 2021; 84:80-88. [PMID: 34757183 DOI: 10.1016/j.semcancer.2021.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
Cancer is characterized by an extremely complex biological background, which hinders personalized therapeutic interventions. Precision medicine promises to overcome this obstacle through integrating information from different 'subsystems', including the host, the external environment, the tumor itself and the tumor micro-environment. Immunogenetics is an essential tool that allows dissecting both lymphoid cancer ontogeny at both a cell-intrinsic and a cell-extrinsic level, i.e. through characterizing micro-environmental interactions, with a view to precision medicine. This is particularly thanks to the introduction of powerful, high-throughput approaches i.e. next generation sequencing, which allow the comprehensive characterization of immune repertoires. Indeed, NGS immunogenetic analysis (Immune-seq) has emerged as key to both understanding cancer pathogenesis and improving the accuracy of clinical decision making in oncology. Immune-seq has applications in lymphoid malignancies, assisting in the diagnosis e.g. through differentiating from reactive conditions, as well as in disease monitoring through accurate assessment of minimal residual disease. Moreover, Immune-seq facilitates the study of T cell receptor clonal dynamics in critical clinical contexts, including transplantation as well as innovative immunotherapy for solid cancers. The clinical utility of Immune-seq represents the focus of the present contribution, where we highlight what can be achieved but also what must be addressed in order to maximally realize the promise of Immune-seq in precision medicine in cancer.
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Affiliation(s)
- Andreas Agathangelidis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisavet Vlachonikola
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Genetics and Molecular Biology, Faculty of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Frederic Davi
- Department of Hematology, APHP, Hôpital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, Rotterdam, the Netherlands
| | - Anastasia Chatzidimitriou
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75236, Sweden.
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6
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Patel DN, Yeagley M, Arturo JF, Falasiri S, Chobrutskiy BI, Gozlan EC, Blanck G. A comparison of immune receptor recombination databases sourced from tumour exome or RNAseq files: Verifications of immunological distinctions between primary and metastatic melanoma. Int J Immunogenet 2021; 48:409-418. [PMID: 34298587 DOI: 10.1111/iji.12550] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023]
Abstract
It became apparent several years ago that RNAseq and exome files prepared from tissue could be mined for adaptive immune receptor (IR) recombinations, which has given extra value to datasets originally intended for gene expression or mutation studies. For example, recovery of IR recombination reads from tumour specimen genomics files can correlate with survival rates. In particular, many benchmarking processes have been applied to the two sets of the IR recombination reads obtained from the cancer genome atlas files, but these two sets have never been directly compared. Here we show that both sets largely agree regarding several parameters. For example, recovery of TRB recombination reads from both WXS and RNAseq files representing metastatic melanoma was associated with a better outcome (p < .0004 in both cases); and T-cell receptor recombination read recovery, for both genomics file types, associated very strongly with T-cell gene expression markers. However, the use of CDR3 chemical features for survival distinctions was not consistent. This topic, and the surprising result that both datasets indicated that primary melanoma with recovery of IR recombination reads, in stark contrast to metastatic melanoma, represents a worse outcome, are discussed.
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Affiliation(s)
- Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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7
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Arndt MF, Koohestani DM, Chobrutskiy BI, Mihyu MM, Diaz M, Gozlan EC, Yeagley M, Zaman S, Roca AM, Blanck G. TRBV and TRBJ usage, when paired with specific HLA alleles, associates with distinct head and neck cancer survival rates. Hum Immunol 2020; 81:692-696. [PMID: 32950267 DOI: 10.1016/j.humimm.2020.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 10/23/2022]
Abstract
Common or dominant, T-cell receptor (TCR), V and J usage, in combination with particular human leukocyte antigen (HLA) alleles, has been associated with differing outcomes in viral infections, autoimmunity, and more recently, in cancer. Cervical cancer in particular represents the most dramatic series of distinctions of outcomes associated with differing combinations of dominant V or J usage and HLA alleles, possibly because of the strong association of cervical cancer with human papilloma virus (HPV), in turn leading to a likely molecular consistency in the mechanism of HPV antigen presentation. Thus, we considered assessing TRB V and J usage, HLA allele combinations, for their associations with survival rates and related data, in the cancer genome atlas head and neck cancer dataset. We obtained the TRB VDJ recombination reads from both the blood and tumor exome files and determined the V and J identities. We then established case ID (patient) subsets of V or J usage, HLA alleles, and determined, for example, that the TRBJ2-7, HLA-B*40:01 combination was associated with a better disease free survival rate than were either the TRBJ1-3, HLA-DPB1*03:01 or the TRBJ2-1, HLA-DPB1*02:01 combinations. Furthermore, these analyses led to the conclusion that TRBJ1-5 usage, and the HLA-C*08:02 and HLA-DRB1*03:01 alleles, had independent associations with distinct overall survival rates. In sum, the results suggest that dominant V or J usage, HLA allele combinations, and in certain cases, dominant V or J usage independently of HLA, could be useful in prognosis and in guiding immunotherapies.
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Affiliation(s)
- Mary F Arndt
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Darush M Koohestani
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Moody M Mihyu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Michael Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Andrea M Roca
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States.
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8
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Wang X, Zhang B, Yang Y, Zhu J, Cheng S, Mao Y, Feng L, Xiao T. Characterization of Distinct T Cell Receptor Repertoires in Tumor and Distant Non-tumor Tissues from Lung Cancer Patients. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:287-296. [PMID: 31479759 PMCID: PMC6818398 DOI: 10.1016/j.gpb.2018.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/12/2018] [Accepted: 10/23/2018] [Indexed: 01/10/2023]
Abstract
T cells and T cell receptors (TCRs) play pivotal roles in adaptive immune responses against tumors. The development of next-generation sequencing technologies has enabled the analysis of the TCRβ repertoire usage. Given the scarce investigations on the TCR repertoire in lung cancer tissues, in this study, we analyzed TCRβ repertoires in lung cancer tissues and the matched distant non-tumor lung tissues (normal lung tissues) from 15 lung cancer patients. Based on our results, the general distribution of T cell clones was similar between cancer tissues and normal lung tissues; however, the proportion of highly expanded clones was significantly higher in normal lung tissues than in cancer tissues (0.021% ± 0.002% vs. 0.016% ± 0.001%, P = 0.0054, Wilcoxon signed rank test). In addition, a significantly higher TCR diversity was observed in cancer tissues than in normal lung tissues (431.37 ± 305.96 vs. 166.20 ± 101.58, P = 0.0075, Mann-Whitney U test). Moreover, younger patients had a significantly higher TCR diversity than older patients (640.7 ± 295.3 vs. 291.8 ± 233.6, P = 0.036, Mann-Whitney U test), and the higher TCR diversity in tumors was significantly associated with worse cancer outcomes. Thus, we provided a comprehensive comparison of the TCR repertoires between cancer tissues and matched normal lung tissues and demonstrated the presence of distinct T cell immune microenvironments in lung cancer patients.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Botao Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yikun Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiawei Zhu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shujun Cheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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9
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Benveniste PM, Nakatsugawa M, Nguyen L, Ohashi PS, Hirano N, Zúñiga-Pflücker JC. In vitro-generated MART-1-specific CD8 T cells display a broader T-cell receptor repertoire than ex vivo naïve and tumor-infiltrating lymphocytes. Immunol Cell Biol 2019; 97:427-434. [PMID: 30633397 DOI: 10.1111/imcb.12231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 12/01/2022]
Abstract
The differentiation of human hematopoietic stem cells into CD8 T cells can be achieved in vitro with the OP9-DL4 system. We considered that in the absence of medullary thymic epithelial cells, which serve to restrict the breath of the T-cell receptor (TCR) repertoire by expressing tissue-restricted antigens, a distinct repertoire would be generated in vitro. To test this notion, we compared the TCR-Vα/Vβ (TRAV/TRBV) gene usage of major histocompatibility complex-restricted antigen (MART-1)-specific T cells generated in vitro to that from ex vivo naïve T cells and tumor-infiltrating lymphocytes (TILs) using high-throughput DNA sequencing. In contrast to naïve T cells and TILs, which showed the expected narrow TRAV repertoire, in vitro-generated MART-1-specific T cells used almost all TRAV gene families and displayed unique CDR3 lengths. Our work demonstrates that the OP9-DL4 system supports the creation of a broad antigen-specific TCR repertoire, suggesting that T cells generated in vitro may undergo a different set of selection events that otherwise constrains the TCR repertoire of thymus-derived T cells.
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Affiliation(s)
| | | | - Linh Nguyen
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Pamela S Ohashi
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Juan Carlos Zúñiga-Pflücker
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada
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10
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Simon S, Wu Z, Cruard J, Vignard V, Fortun A, Khammari A, Dreno B, Lang F, Rulli SJ, Labarriere N. TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires: Common and Specific Features. Front Immunol 2018; 9:1962. [PMID: 30214446 PMCID: PMC6125394 DOI: 10.3389/fimmu.2018.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Among Immunotherapeutic approaches for cancer treatment, the adoptive transfer of antigen specific T cells is still a relevant approach, that could have higher efficacy when further combined with immune check-point blockade. A high number of adoptive transfer trials have been performed in metastatic melanoma, due to its high immunogenic potential, either with polyclonal TIL or antigen-specific polyclonal populations. In this setting, the extensive characterization of T cell functions and receptor diversity of infused polyclonal T cells is required, notably for monitoring purposes. We developed a clinical grade procedure for the selection and amplification of polyclonal CD8 T cells, specific for two shared and widely expressed melanoma antigens: Melan-A and MELOE-1. This procedure is currently used in a clinical trial for HLA-A2 metastatic melanoma patients. In this study, we characterized the T-cell diversity (T-cell repertoire) of such T cell populations using a new RNAseq strategy. We first assessed the added-value of TCR receptor sequencing, in terms of sensitivity and specificity, by direct comparison with cytometry analysis of the T cell populations labeled with anti-Vß-specific antibodies. Results from these analyzes also confirmed specific features already reported for Melan-A and MELOE-1 specific T cell repertoires in terms of V-alpha recurrence usage, on a very high number of T cell clonotypes. Furthermore, these analyses also revealed undescribed features, such as the recurrence of a specific motif in the CDR3α region for MELOE-1 specific T cell repertoire. Finally, the analysis of a large number of T cell clonotypes originating from various patients revealed the existence of public CDR3α and ß clonotypes for Melan-A and MELOE-1 specific T cells. In conclusion, this method of high throughput TCR sequencing is a reliable and powerful approach to deeply characterize polyclonal T cell repertoires, and to reveal specific features of a given TCR repertoire, that would be useful for immune follow-up of cancer patients treated by immunotherapeutic approaches.
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Affiliation(s)
- Sylvain Simon
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Zhong Wu
- Qiagen Sciences, Frederick, MD, United States
| | - J Cruard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Virginie Vignard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Agnes Fortun
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Amir Khammari
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Department of Dermato-Cancerology of Nantes Hospital, Nantes, France
| | - Brigitte Dreno
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Department of Dermato-Cancerology of Nantes Hospital, Nantes, France
| | - Francois Lang
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | | | - Nathalie Labarriere
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Centre Hospitalier Universitaire Nantes, Nantes, France
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11
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Faghih Z, Deihimi S, Talei A, Ghaderi A, Erfani N. Analysis of T cell receptor repertoire based on Vβ chain in patients with breast cancer. Cancer Biomark 2018; 22:733-745. [DOI: 10.3233/cbm-181295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zahra Faghih
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safoora Deihimi
- Perelman School of Medicine, University of Pennsylvania, Abramson Cancer Center, Philadelphia, PA, USA
| | - Abdolrasoul Talei
- Breast Disease Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrollah Erfani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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12
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Bovay A, Zoete V, Dolton G, Bulek AM, Cole DK, Rizkallah PJ, Fuller A, Beck K, Michielin O, Speiser DE, Sewell AK, Fuertes Marraco SA. T cell receptor alpha variable 12-2 bias in the immunodominant response to Yellow fever virus. Eur J Immunol 2018; 48:258-272. [PMID: 28975614 PMCID: PMC5887915 DOI: 10.1002/eji.201747082] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/15/2017] [Accepted: 09/25/2017] [Indexed: 12/12/2022]
Abstract
The repertoire of human αβ T-cell receptors (TCRs) is generated via somatic recombination of germline gene segments. Despite this enormous variation, certain epitopes can be immunodominant, associated with high frequencies of antigen-specific T cells and/or exhibit bias toward a TCR gene segment. Here, we studied the TCR repertoire of the HLA-A*0201-restricted epitope LLWNGPMAV (hereafter, A2/LLW) from Yellow Fever virus, which generates an immunodominant CD8+ T cell response to the highly effective YF-17D vaccine. We discover that these A2/LLW-specific CD8+ T cells are highly biased for the TCR α chain TRAV12-2. This bias is already present in A2/LLW-specific naïve T cells before vaccination with YF-17D. Using CD8+ T cell clones, we show that TRAV12-2 does not confer a functional advantage on a per cell basis. Molecular modeling indicated that the germline-encoded complementarity determining region (CDR) 1α loop of TRAV12-2 critically contributes to A2/LLW binding, in contrast to the conventional dominant dependence on somatically rearranged CDR3 loops. This germline component of antigen recognition may explain the unusually high precursor frequency, prevalence and immunodominance of T-cell responses specific for the A2/LLW epitope.
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Affiliation(s)
- Amandine Bovay
- Department of OncologyLausanne University Hospital (CHUV)EpalingesSwitzerland
| | - Vincent Zoete
- SIB Swiss Institute of BioinformaticsMolecular Modeling GroupLausanneSwitzerland
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research InstituteCardiff University School of MedicineHeath ParkCardiffUK
| | - Anna M. Bulek
- Division of Infection and Immunity and Systems Immunity Research InstituteCardiff University School of MedicineHeath ParkCardiffUK
| | - David K. Cole
- Division of Infection and Immunity and Systems Immunity Research InstituteCardiff University School of MedicineHeath ParkCardiffUK
| | - Pierre J. Rizkallah
- Division of Infection and Immunity and Systems Immunity Research InstituteCardiff University School of MedicineHeath ParkCardiffUK
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research InstituteCardiff University School of MedicineHeath ParkCardiffUK
| | - Konrad Beck
- Cardiff University School of DentistryHeath ParkCardiffUK
| | - Olivier Michielin
- SIB Swiss Institute of BioinformaticsMolecular Modeling GroupLausanneSwitzerland
| | - Daniel E. Speiser
- Department of OncologyLausanne University Hospital (CHUV)EpalingesSwitzerland
| | - Andrew K. Sewell
- Division of Infection and Immunity and Systems Immunity Research InstituteCardiff University School of MedicineHeath ParkCardiffUK
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13
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Abstract
PURPOSE OF REVIEW The genetic susceptibility and dominant protection for type 1 diabetes (T1D) associated with human leukocyte antigen (HLA) haplotypes, along with minor risk variants, have long been thought to shape the T cell receptor (TCR) repertoire and eventual phenotype of autoreactive T cells that mediate β-cell destruction. While autoantibodies provide robust markers of disease progression, early studies tracking autoreactive T cells largely failed to achieve clinical utility. RECENT FINDINGS Advances in acquisition of pancreata and islets from T1D organ donors have facilitated studies of T cells isolated from the target tissues. Immunosequencing of TCR α/β-chain complementarity determining regions, along with transcriptional profiling, offers the potential to transform biomarker discovery. Herein, we review recent studies characterizing the autoreactive TCR signature in T1D, emerging technologies, and the challenges and opportunities associated with tracking TCR molecular profiles during the natural history of T1D.
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Affiliation(s)
- Laura M Jacobsen
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Amanda Posgai
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA.
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14
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Madi A, Poran A, Shifrut E, Reich-Zeliger S, Greenstein E, Zaretsky I, Arnon T, Laethem FV, Singer A, Lu J, Sun PD, Cohen IR, Friedman N. T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences. eLife 2017; 6. [PMID: 28731407 PMCID: PMC5553937 DOI: 10.7554/elife.22057] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 07/14/2017] [Indexed: 01/09/2023] Open
Abstract
Diversity of T cell receptor (TCR) repertoires, generated by somatic DNA rearrangements, is central to immune system function. However, the level of sequence similarity of TCR repertoires within and between species has not been characterized. Using network analysis of high-throughput TCR sequencing data, we found that abundant CDR3-TCRβ sequences were clustered within networks generated by sequence similarity. We discovered a substantial number of public CDR3-TCRβ segments that were identical in mice and humans. These conserved public sequences were central within TCR sequence-similarity networks. Annotated TCR sequences, previously associated with self-specificities such as autoimmunity and cancer, were linked to network clusters. Mechanistically, CDR3 networks were promoted by MHC-mediated selection, and were reduced following immunization, immune checkpoint blockade or aging. Our findings provide a new view of T cell repertoire organization and physiology, and suggest that the immune system distributes its TCR sequences unevenly, attending to specific foci of reactivity. DOI:http://dx.doi.org/10.7554/eLife.22057.001
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Affiliation(s)
- Asaf Madi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Asaf Poran
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Irena Zaretsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Arnon
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Department of Physics and Astronomy, Alfred University, Alfred, United States
| | - Francois Van Laethem
- Experimental Immunology Branch, National Cancer Institute, Bethesda, United States
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer Institute, Bethesda, United States
| | - Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, United States
| | - Peter D Sun
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, United States
| | - Irun R Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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15
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Tickotsky N, Sagiv T, Prilusky J, Shifrut E, Friedman N. McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences. Bioinformatics 2017; 33:2924-2929. [DOI: 10.1093/bioinformatics/btx286] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/02/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nili Tickotsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Sagiv
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prilusky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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16
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CD8 + T cells specific for the islet autoantigen IGRP are restricted in their T cell receptor chain usage. Sci Rep 2017; 7:44661. [PMID: 28300170 PMCID: PMC5353542 DOI: 10.1038/srep44661] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/13/2017] [Indexed: 11/21/2022] Open
Abstract
CD8+ T cells directed against beta cell autoantigens are considered relevant for the pathogenesis of type 1 diabetes. Using single cell T cell receptor sequencing of CD8+ T cells specific for the IGRP265-273 epitope, we examined whether there was expansion of clonotypes and sharing of T cell receptor chains in autoreactive CD8+ T cell repertoires. HLA-A*0201 positive type 1 diabetes patients (n = 19) and controls (n = 18) were analysed. TCR α- and β-chain sequences of 418 patient-derived IGRP265-273-multimer+ CD8+ T cells representing 48 clonotypes were obtained. Expanded populations of IGRP265-273-specific CD8+ T cells with dominant clonotypes that had TCR α-chains shared across patients were observed. The SGGSNYKLTF motif corresponding to TRAJ53 was contained in 384 (91.9%) cells, and in 20 (41.7%) patient-derived clonotypes. TRAJ53 together with TRAV29/DV5 was found in 15 (31.3%) clonotypes. Using next generation TCR α-chain sequencing, we found enrichment of one of these TCR α-chains in the memory CD8+ T cells of patients as compared to healthy controls. CD8+ T cell clones bearing the enriched motifs mediated antigen-specific target cell lysis. We provide the first evidence for restriction of T cell receptor motifs in the alpha chain of human CD8+ T cells with specificity to a beta cell antigen.
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17
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Frankl JA, Thearle MS, Desmarais C, Bogardus C, Krakoff J. T-cell receptor repertoire variation may be associated with type 2 diabetes mellitus in humans. Diabetes Metab Res Rev 2016; 32:297-307. [PMID: 26408818 PMCID: PMC6383518 DOI: 10.1002/dmrr.2720] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/07/2015] [Accepted: 08/23/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recent work in Pima Indians, a population with high rates of obesity and type 2 diabetes mellitus (T2DM), demonstrated that human leukocyte antigen haplotype DRB1*02 carriers have an increased acute insulin response and decreased risk for the development of T2DM, implicating loss of self-tolerance in the pathogenesis of T2DM. Advances in genomic sequencing have made T-cell receptor repertoire analysis a practical mode of investigation. METHODS High-throughput sequencing of T-cell receptor complementarity-determining region 3 was carried out in male Pima Indians with normal glucose regulation (n = 11; age = 31 ± 8 years; %fat = 30.2 ± 8.7%) and the protective DRB1*02 haplotype versus those with T2DM without DRB1*02 (n = 7; age = 34 ± 8 years; %fat = 31.2 ± 4.7%). Findings were partially replicated in another cohort by assessing the predictive ability of T-cell receptor variation on risk of T2DM in Pima Indian men (n = 27; age = 28.9 ± 7.1 years; %fat = 28.8 ± 7.1%) and women (n = 20; age = 29 ± 7.0 years; %fat = 37.1 ± 6.8%) with baseline normal glucose regulation but without the protective haplotype who were invited to follow-up examinations as frequently as every 2 years where diabetes status was assessed by a 75-g oral glucose tolerance test. Of these subjects, 13 developed diabetes. RESULTS T-cell receptor complementarity-determining region 3 length was shorter in those with T2DM, and a one-nucleotide decrease in complementarity-determining region 3 length was associated with a nearly threefold increase in risk for future diabetes. The frequency of one variable gene, TRBV7-8, was higher in those with T2DM. A 1% increase in TRBV7-8 frequency was associated with a greater than threefold increase in diabetes risk. CONCLUSIONS These results indicate that T-cell autoimmunity may be an important component in progression to T2DM in Pima Indians.
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Affiliation(s)
- Joseph A. Frankl
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Marie S. Thearle
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | | | - Clifton Bogardus
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Jonathan Krakoff
- Obesity and Diabetes Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
- Correspondence to: Jonathan Krakoff, 5th Floor, Phoenix Indian Medical Center, 4212 N. 16th St, Phoenix, AZ 85016, USA.
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18
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CDR3β sequence motifs regulate autoreactivity of human invariant NKT cell receptors. J Autoimmun 2015; 68:39-51. [PMID: 26748722 DOI: 10.1016/j.jaut.2015.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 11/22/2022]
Abstract
Invariant natural killer T (iNKT) cells are a subset of T lymphocytes that recognize lipid ligands presented by monomorphic CD1d. Human iNKT T cell receptor (TCR) is largely composed of invariant Vα24 (Vα24i) TCRα chain and semi-variant Vβ11 TCRβ chain, where complementarity-determining region (CDR)3β is the sole variable region. One of the characteristic features of iNKT cells is that they retain autoreactivity even after the thymic selection. However, the molecular features of human iNKT TCR CDR3β sequences that regulate autoreactivity remain unknown. Since the numbers of iNKT cells with detectable autoreactivity in peripheral blood is limited, we introduced the Vα24i gene into peripheral T cells and generated a de novo human iNKT TCR repertoire. By stimulating the transfected T cells with artificial antigen presenting cells (aAPCs) presenting self-ligands, we enriched strongly autoreactive iNKT TCRs and isolated a large panel of human iNKT TCRs with a broad range autoreactivity. From this panel of unique iNKT TCRs, we deciphered three CDR3β sequence motifs frequently encoded by strongly-autoreactive iNKT TCRs: a VD region with 2 or more acidic amino acids, usage of the Jβ2-5 allele, and a CDR3β region of 13 amino acids in length. iNKT TCRs encoding 2 or 3 sequence motifs also exhibit higher autoreactivity than those encoding 0 or 1 motifs. These data facilitate our understanding of the molecular basis for human iNKT cell autoreactivity involved in immune responses associated with human disease.
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19
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Jia Q, Zhou J, Chen G, Shi Y, Yu H, Guan P, Lin R, Jiang N, Yu P, Li QJ, Wan Y. Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer. Oncoimmunology 2015; 4:e1001230. [PMID: 26137399 DOI: 10.1080/2162402x.2014.1001230] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 12/22/2022] Open
Abstract
A characteristic immunopathology of human cancers is the induction of tumor antigen-specific T lymphocyte responses within solid tumor tissues. Current strategies for immune monitoring focus on the quantification of the density and differentiation status of tumor-infiltrating T lymphocytes; however, properties of the TCR repertoire ‒ including antigen specificity, clonality, as well as its prognostic significance ‒ remain elusive. In this study, we enrolled 28 gastric cancer patients and collected tumor tissues, adjacent normal mucosal tissues, and peripheral blood samples to study the landscape and compartmentalization of these patients' TCR β repertoire by deep sequencing analyses. Our results illustrated antigen-driven expansion within the tumor compartment and the contracted size of shared clonotypes in mucosa and peripheral blood. Most importantly, the diversity of mucosal T lymphocytes could independently predict prognosis, which strongly underscores critical roles of resident mucosal T-cells in executing post-surgery immunosurveillance against tumor relapse.
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Affiliation(s)
- Qingzhu Jia
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China ; Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Junfeng Zhou
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China
| | - Gang Chen
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Yan Shi
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China
| | - Haili Yu
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Peng Guan
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Regina Lin
- Department of Immunology; Duke University Medical Center ; Durham, NC USA
| | - Ning Jiang
- Department of Biomedical Engineering; Cockrell School of Engineering; University of Texas at Austin ; Austin, TX USA
| | - Peiwu Yu
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China
| | - Qi-Jing Li
- Chongqing Key Laboratory of Cellomics ; Chongqing, China ; Department of Immunology; Duke University Medical Center ; Durham, NC USA
| | - Ying Wan
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
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20
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Sainz-Perez A, Lim A, Lemercier B, Leclerc C. The T-cell receptor repertoire of tumor-infiltrating regulatory T lymphocytes is skewed toward public sequences. Cancer Res 2012; 72:3557-69. [PMID: 22573714 DOI: 10.1158/0008-5472.can-12-0277] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The accumulation of CD4(+) T regulatory cells (Treg) in tumor tissue is a widely described phenomenon in mouse models and in human cancer patients. Understanding the mechanisms by which Treg migrate and accumulate in tumors is important because they strongly influence the potential efficacy of many immunotherapies. In this study, we used immunoscope technology to analyze the T-cell receptor (TCR) repertoire of tumor-infiltrating T cells in non-TCR transgenic mice. Both tumor-infiltrating Tregs and T effector cells (Teff) displayed sequence profiles in the CDR3 region that were characteristic of biased repertoires seen during clonal cell expansions, implying that strong T-cell responses have occurred within the tumor tissue. By comparing the TCR sequences of tumor-infiltrating Tregs, we obtained evidence of the presence of so-called public TCR sequences that are common to many individuals yet were tumor-specific in nature. Such comparisons also suggested that the Treg-Teff conversion process is not an active process at the tumor site or tumor-draining lymph nodes. Our findings strongly suggest that Treg infiltration of tumor tissue is followed by marked proliferation of a few dominant T-cell clones in the tumor.
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Affiliation(s)
- Alexander Sainz-Perez
- Institut Pasteur, Immune Regulation and Vaccinology Unit, Department of Immunology, Paris, France
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21
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Ochsenreither S, Fusi A, Geikowski A, Stather D, Busse A, Stroux A, Letsch A, Keilholz U. Wilms' tumor protein 1 (WT1) peptide vaccination in AML patients: predominant TCR CDR3β sequence associated with remission in one patient is detectable in other vaccinated patients. Cancer Immunol Immunother 2012; 61:313-22. [PMID: 21898091 PMCID: PMC11029123 DOI: 10.1007/s00262-011-1099-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 08/13/2011] [Indexed: 12/01/2022]
Abstract
BACKGROUND Clinically effective T-cell responses can be elicited by single peptide vaccination with Wilms' tumor 1 (WT1) epitope 126-134 in patients with acute myeloid leukemia (AML). We recently showed that a predominant T-cell receptor (TCR) β chain was associated with vaccine-induced complete remission in an AML patient (patient 1). In this study, we address the question of whether this predominant clone or the accompanying Vβ11 restriction could be found in other AML patients vaccinated with the same WT1 peptide. MATERIALS AND METHODS For assessment of Vβ usage, cytotoxic T lymphocytes (CTLs) from four vaccinated patients were divided into specific and non-specific by epitope-specific enrichment. Vβ families were quantified in both fractions using reverse transcribed quantitative PCR. Vβ11-positive 'complementary determining region 3' (CDR3) sequences were amplified from these samples, from bone marrow samples of 17 other vaccination patients, and from peripheral blood of six healthy controls, cloned and sequenced. RESULTS We observed a clear bias towards Vβ11 usage of the WT1-specific CTL populations in all four patients. The predominant CDR3β amino acid (AA) sequence of patient 1 was detected in two other patients. CDR3β loops with closely related AA sequences were only found in patient 1. There were no CDR3β AA sequences with side chains of identical chemical properties detected in any patient. CONCLUSION We provide the first data addressing TCR Vβ chain usage in WT1-specific T-cell populations after HLA A*0201-restricted single peptide vaccination. We demonstrate both shared Vβ restriction and the sharing of a TCR β transcript with proven clinical impact in one patient.
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MESH Headings
- Acute Disease
- Adult
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Cancer Vaccines/administration & dosage
- Cancer Vaccines/immunology
- Clone Cells/immunology
- Clone Cells/metabolism
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Epitopes/immunology
- Female
- HLA-A2 Antigen/immunology
- Humans
- Leukemia, Myeloid/immunology
- Leukemia, Myeloid/therapy
- Male
- Middle Aged
- Molecular Sequence Data
- Peptide Fragments/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Remission Induction
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Vaccination
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/immunology
- WT1 Proteins/chemistry
- WT1 Proteins/immunology
- Young Adult
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Affiliation(s)
- Sebastian Ochsenreither
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Alberto Fusi
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anne Geikowski
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - David Stather
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Antonia Busse
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Andrea Stroux
- Institute for Biometry and Clinical Epidemiology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anne Letsch
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Ulrich Keilholz
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
- Department of Medicine III, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
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22
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Abstract
Historically, sharing T cell receptors (TCRs) between individuals has been speculated to be impossible, considering the dramatic discrepancy between the potential enormity of the TCR repertoire and the limited number of T cells generated in each individual. However, public T cell response, in which multiple individuals share identical TCRs in responding to a same antigenic epitope, has been extensively observed in a variety of immune responses across many species. Public T cell responses enable individuals within a population to generate similar antigen-specific TCRs against certain ubiquitous pathogens, leading to favorable biological outcomes. However, the relatively concentrated feature of TCR repertoire may limit T cell response in a population to some other pathogens. It could be a great benefit for human health if public T cell responses can be manipulated. Therefore, the mechanistic insight of public TCR generation is important to know. Recently, high-throughput DNA sequencing has revolutionized the study of immune receptor repertoires, which allows a much better understanding of the factors that determine the overlap of TCR repertoire among individuals. Here, we summarize the current knowledge on public T-cell response and discuss future challenges in this field.
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Affiliation(s)
- Hanjie Li
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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23
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Miles JJ, Douek DC, Price DA. Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol Cell Biol 2011; 89:375-87. [PMID: 21301479 DOI: 10.1038/icb.2010.139] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The naïve T-cell repertoire is vast, containing millions of unique T-cell receptor (TCR) structures. Faced with such diversity, the mobilization of TCR structures from this enormous pool was once thought to be a stochastic, even chaotic, process. However, steady and systematic dissection over the last 20 years has revealed that this is not the case. Instead, the TCR repertoire deployed against individual antigens is routinely ordered and biased. Often, identical and near-identical TCR repertoires can be observed across different individuals, suggesting that the system encompasses an element of predictability. This review provides a catalog of αβ TCR bias by disease and by species, and discusses the mechanisms that govern this inherent and widespread phenomenon.
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Affiliation(s)
- John J Miles
- T Cell Modulation Laboratory, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, UK.
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24
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Zuleger CL, Macklin MD, Bostwick BL, Pei Q, Newton MA, Albertini MR. In vivo 6-thioguanine-resistant T cells from melanoma patients have public TCR and share TCR beta amino acid sequences with melanoma-reactive T cells. J Immunol Methods 2010; 365:76-86. [PMID: 21182840 DOI: 10.1016/j.jim.2010.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 12/01/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
In vivo hypoxanthine-guanine phosphoribosyltransferase (HPRT)-deficient T cells (MT) from melanoma patients are enriched for T cells with in vivo clonal amplifications that traffic between blood and tumor tissues. Melanoma is thus a model cancer to test the hypothesis that in vivo MT from cancer patients can be used as immunological probes for immunogenic tumor antigens. MT were obtained by 6-thioguanine (TG) selection of lymphocytes from peripheral blood and tumor tissues, and wild-type T cells (WT) were obtained analogously without TG selection. cDNA sequences of the T cell receptor beta chains (TRB) were used as unambiguous biomarkers of in vivo clonality and as indicators of T cell specificity. Public TRB were identified in MT from the blood and tumor of different melanoma patients. Such public TRB were not found in normal control MT or WT. As an indicator of T cell specificity for melanoma, the >2600 MT and WT TRB, including the public TRB from melanoma patients, were compared to a literature-derived empirical database of >1270 TRB from melanoma-reactive T cells. Various degrees of similarity, ranging from 100% conservation to 3-amino acid motifs (3-mer), were found between both melanoma patient MT and WT TRBs and the empirical database. The frequency of 3-mer and 4-mer TRB matching to the empirical database was significantly higher in MT compared with WT in the tumor (p=0.0285 and p=0.006, respectively). In summary, in vivo MT from melanoma patients contain public TRB as well as T cells with specificity for characterized melanoma antigens. We conclude that in vivo MT merit study as novel probes for uncharacterized immunogenic antigens in melanoma and other malignancies.
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Profile of a serial killer: cellular and molecular approaches to study individual cytotoxic T-cells following therapeutic vaccination. J Biomed Biotechnol 2010; 2011:452606. [PMID: 21113290 PMCID: PMC2989374 DOI: 10.1155/2011/452606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 09/29/2010] [Indexed: 12/28/2022] Open
Abstract
T-cell vaccination may prevent or treat cancer and infectious diseases, but further progress is required to increase clinical efficacy. Step-by-step improvements of T-cell vaccination in phase I/II clinical studies combined with very detailed analysis of T-cell responses at the single cell level are the strategy of choice for the identification of the most promising vaccine candidates for testing in subsequent large-scale phase III clinical trials. Major aims are to fully identify the most efficient T-cells in anticancer therapy, to characterize their TCRs, and to pinpoint the mechanisms of T-cell recruitment and function in well-defined clinical situations. Here we discuss novel strategies for the assessment of human T-cell responses, revealing in part unprecedented insight into T-cell biology and novel structural principles that govern TCR-pMHC recognition. Together, the described approaches advance our knowledge of T-cell mediated-protection from human diseases.
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Subramanya S, Armant M, Salkowitz JR, Nyakeriga AM, Haridas V, Hasan M, Bansal A, Goepfert PA, Wynn KK, Ladell K, Price DA, N M, Kan-Mitchell J, Shankar P. Enhanced induction of HIV-specific cytotoxic T lymphocytes by dendritic cell-targeted delivery of SOCS-1 siRNA. Mol Ther 2010; 18:2028-37. [PMID: 20648001 PMCID: PMC2990509 DOI: 10.1038/mt.2010.148] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 06/15/2010] [Indexed: 12/24/2022] Open
Abstract
Dendritic cells (DCs) are potent antigen-presenting cells that play a critical role in the activation of T cells. RNA interference (RNAi)-mediated silencing of negative immunoregulatory molecules expressed by DCs may provide a strategy to enhance the potency of DC-based vaccines and immunotherapy. Ablation of suppressor of cytokine signaling-1 (SOCS-1) in antigen-presenting cells has been shown to enhance cellular immune response in mice. Here, we used a previously reported DC-targeting approach to deliver small interfering RNA (siRNA) against SOCS-1 to human myeloid-derived DCs (MDDCs). SOCS1-silencing in MDDCs resulted in enhanced cytokine responses to lipopolysaccharide (LPS) and a strong mixed-lymphocyte reaction. Moreover, only DCs treated with SOCS-1 siRNA, and not controls, elicited strong primary in vitro responses to well-characterized HLA-A*0201-restricted Melan-A/MART-1 and human immunodeficiency virus (HIV) Gag epitopes in naive CD8(+) T cells from healthy donors. Finally, stimulation of CD8(+) T cells from HIV-seropositive subjects with SOCS1-silenced DCs resulted in an augmented polyfunctional cytotoxic T-lymphocyte (CTL) response, suggesting that SOCS-1 silencing can restore functionally compromised T cells in HIV infection. Collectively, these results demonstrate the feasibility of DC3-9dR-mediated manipulation of DC function to enhance DC immunogenicity for potential vaccine or immunotherapeutic applications.
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Affiliation(s)
- Sandesh Subramanya
- Immune Disease Institute, Harvard Medical School, Boston, Massachusetts, USA
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Palermo B, Del Bello D, Sottini A, Serana F, Ghidini C, Gualtieri N, Ferraresi V, Catricalà C, Belardelli F, Proietti E, Natali PG, Imberti L, Nisticò P. Dacarbazine Treatment before Peptide Vaccination Enlarges T-Cell Repertoire Diversity of Melan-A–Specific, Tumor-Reactive CTL in Melanoma Patients. Cancer Res 2010; 70:7084-92. [DOI: 10.1158/0008-5472.can-10-1326] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cole DK, Edwards ESJ, Wynn KK, Clement M, Miles JJ, Ladell K, Ekeruche J, Gostick E, Adams KJ, Skowera A, Peakman M, Wooldridge L, Price DA, Sewell AK. Modification of MHC anchor residues generates heteroclitic peptides that alter TCR binding and T cell recognition. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 185:2600-10. [PMID: 20639478 PMCID: PMC3024538 DOI: 10.4049/jimmunol.1000629] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Improving T cell Ags by altering MHC anchor residues is a common strategy used to enhance peptide vaccines, but there has been little assessment of how such modifications affect TCR binding and T cell recognition. In this study, we use surface plasmon resonance and peptide-MHC tetramer binding at the cell surface to demonstrate that changes in primary peptide anchor residues can substantially and unpredictably alter TCR binding. We also demonstrate that the ability of TCRs to differentiate between natural and anchor-modified heteroclitic peptides distinguishes T cells that exhibit a strong preference for either type of Ag. Furthermore, we show that anchor-modified heteroclitic peptides prime T cells with different TCRs compared with those primed with natural Ag. Thus, vaccination with heteroclitic peptides may elicit T cells that exhibit suboptimal recognition of the intended natural Ag and, consequently, impaired functional attributes in vivo. Heteroclitic peptide-based immune interventions therefore require careful evaluation to ensure efficacy in the clinic.
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MESH Headings
- Amino Acid Sequence
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cells, Cultured
- Cytokines/immunology
- Cytokines/metabolism
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Flow Cytometry
- HLA-A Antigens/genetics
- HLA-A Antigens/immunology
- HLA-A Antigens/metabolism
- HLA-A2 Antigen
- Humans
- Mutation
- Oligopeptides/genetics
- Oligopeptides/immunology
- Oligopeptides/metabolism
- Peptide Library
- Protein Binding/immunology
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Surface Plasmon Resonance
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- David K Cole
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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Wieckowski S, Baumgaertner P, Corthesy P, Voelter V, Romero P, Speiser DE, Rufer N. Fine structural variations of alphabetaTCRs selected by vaccination with natural versus altered self-antigen in melanoma patients. THE JOURNAL OF IMMUNOLOGY 2009; 183:5397-406. [PMID: 19786555 DOI: 10.4049/jimmunol.0901460] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Immunotherapy of cancer is often performed with altered "analog" peptide Ags optimized for HLA class I binding, resulting in enhanced immunogenicity, but the induced T cell responses require further evaluation. Recently, we demonstrated fine specificity differences and enhanced recognition of naturally presented Ag by T cells after vaccination with natural Melan-A/MART-1 peptide, as compared with analog peptide. In this study, we compared the TCR primary structures of 1489 HLA-A*0201/Melan-A(26-35)-specific CD8 T cells derived from both cohorts of patients. Although a strong preference for TRAV12-2 segment usage was present in nearly all patients, usage of particular TRAJ gene segments and CDR3alpha composition differed slightly after vaccination with natural vs analog peptide. Moreover, TCR beta-chain repertoires were broader after natural than analog peptide vaccination. In all patients, we observed a marked conservation of the CDR3beta amino acid composition with recurrent sequences centered on a glycyl-leucyl/valyl/alanyl-glycyl motif. In contrast to viral-specific TCR repertoires, such "public" motifs were primarily expressed by nondominant T cell clonotypes, which contrasted with "private" CDR3beta signatures frequently found in T cell clonotypes that dominated repertoires of individual patients. Interestingly, no differences in functional avidity were observed between public and private T cell clonotypes. Collectively, our data indicate that T cell repertoires generated against natural or analog Melan-A peptide exhibited slightly distinct but otherwise overlapping and structurally conserved TCR features, suggesting that the differences in binding affinity/avidity of TCRs toward pMHC observed in the two cohorts of patients are caused by subtle structural TCR variations.
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Affiliation(s)
- Sébastien Wieckowski
- Division of Experimental Oncology, Multidisciplinary Oncology Center, Lausanne University Hospital, Lausanne, Switzerland
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